Electrofishing data for eel (Anguilla anguilla) in the SUDOE area

1. DESCRIPTION

        1.1.     THE SUDOANG PROJECT

The SUDOANG project aims at providing common tools to managers to support eel conservation in the SUDOE area (Spain, France and Portugal). 

Three main datasets have been used to implement EDA.

A database of rivers and their attributes along with tools for chaining.

A database of dams.

A database of electrofishing (current dataset).

Electrofishing data include site locations, fishing operations which can be done several times at one site, and fish data collected during each operation. The operations are attached to stretches of river or river segments whose characteristics describe the conditions for presence, density, size structure, or silvering rate of the eels. 

The electrofishing operation are classified by type, com full two pass fishing, coa full two pass electrofishing for eel,  iaa eel abundance point sampling, ber bank sampling gm point fishing for large streams oth other, or unspecified.

         1.2.     TEMPORAL SCOPE 

From 1985 to 2018, beware  incomplete dataset after 2015 in France.

         1.3.      GEOGRAPHICAL RANGE

The SUDOE area including Iberian Peninsula and France.

2. DATASETS DESCRIPTION

2.1. DENSITIES AND PRESENCE ABSENCE

dataset :  frsppt_12_2020.Rdata

Most variables are built here 

The script to create cumulated values for dams can be found here

For a technical description see the report

Contains :

ddd => dataset used to calibrate the presence absence model, 46147 lines

ddg => dataset used to calibrate the gamma model (only positive values retained), 19993 lines.

tdd => dataset corresponding to places where transport operation have been identified, presence absence model, 6582 lines.

tdg => dataset corresponding to places where transport operation have been identified, gamma model (only positive values) 984 lines.

And the following columns (in alphabetical order) :

altitudem.

Altitude in meter truncated to 800 m

area_sudo

Area for recruitment (Drouineau et al., 2021)

codesea

Code of the Sea, factor A = Atlantic, M = Mediterranean

country

A factor (FR, SP, PT) for France, Portugral and Spain

country2

Country with grouping for the Iberian Peninsula, levels: FR SPPT

cs_height_08_n

Cumulated height from the sea,  dam height transformed with power 0.8, no prediction for missing values.

cs_height_08_n.

Same variable but truncated to 300

cs_height_08_p

Cumulated height from the sea,  dam height transformed with power 0.8, with prediction for missing values.

cs_height_08_p.

Same variable but truncated to 300

cs_height_08_pp

Cumulated height from the sea,  dam height transformed with power 0.8, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel

cs_height_08_pps

Cumulated height from the sea,  dam height transformed with power 0.8, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure

cs_height_10_FR

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from France are considered when building on a transnational water course.

cs_height_10_n

Cumulated height from the sea, no transformation, no prediction for missing values.

cs_height_10_n.

Same variable but truncated to 200

cs_height_10_p

Cumulated height from the sea, no transformation, missing height are extrapolated from two different models in France and the Iberian Peninsula

cs_height_10_p.

Same variable but truncated to 200

cs_height_10_pass0

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams without pass are used to build the cumulated value.

cs_height_10_pass1

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams with pass are used to build the cumulated value.

cs_height_10_pp

Cumulated height from the sea, no transformation,  with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel

cs_height_10_ppass0

Cumulated height from the sea, no transformation, including prediction for missing values, only the dams without pass are used to build the cumulated value.

cs_height_10_ppass1

Cumulated height from the sea, no transformation, including prediction for missing values, only the dams with pass are used to build the cumulated value.

cs_height_10_pps

Cumulated height from the sea, no transformation,  with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure

cs_height_10_pscore0

Cumulated height from the sea, no transformation, including prediction for missing values, only the dams without score are used to build the cumulated value.

cs_height_10_pscore1

Cumulated height from the sea, no transformation, including prediction for missing values, only the dams with score (that have been expertised as no or small barrier for eel)  are used to build the cumulated value.

cs_height_10_PT

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from Portugal are considered when building on a transnational water course.

cs_height_10_score0

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams without score are used to build the cumulated value.

cs_height_10_score1

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams with score (that have been expertised as no or small barrier for eel)  are used to build the cumulated value.

cs_height_10_SP

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from Spain are considered when building on a transnational water course.

cs_height_12_n

Cumulated height from the sea,  dam height transformed with power 1.2, no prediction for missing values.

cs_height_12_n.

Same variable but truncated to 500

cs_height_12_p

Cumulated height from the sea,  dam height transformed with power 1.2, with prediction for missing values.

cs_height_12_p.

Same variable but truncated to 500

cs_height_12_pp

Cumulated height from the sea,  dam height transformed with power 1.2, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel

cs_height_12_pps

Cumulated height from the sea,  dam height transformed with power 1.2, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure

cs_height_15_n

Cumulated height from the sea,  dam height transformed with power 1.5, no prediction for missing values.

cs_height_15_n.

Same variable but truncated to 800

cs_height_15_p

Cumulated height from the sea,  dam height transformed with power 1.5, with prediction for missing values.

cs_height_15_p.

Same variable but truncated to 800

cs_height_15_pp

Cumulated height from the sea,  dam height transformed with power 1.5, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel

cs_height_15_pps

Cumulated height from the sea,  dam height transformed with power 1.5, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure

cumnbdamp

Cumulated number of dam from the sea

cumnbdamso

duplicate of cumnbdamp

cumwettedsurfacebothkm2.

Surface of water downstream from the segment in the river. Corresponds to both riversegment and waterbodies.

cumwettedsurfacekm2.

Surface of water downstream from the segment in the river. Corresponds only to rivers

cumwettedsurfaceotherkm2.

Surface of water downstream from the segment in the river. Corresponds only waterbodies (water surfaces, associated with the segment).

densCS

Density from Carle and Strub, number in second pass extrapolated from efficiency if only one pass.

dist_from_gibraltar_km

Distance to Gibraltar calculated using an enveloppe along the coastline (e.g. the estuaries ingress inland are not counted for this distance).

distanceseakm

Distance to the sea

distanceseakm.

Distance to the sea, truncated at 500

distancesourcem

distance to the source in m

downstdrainagewettedsurfaceboth.

Percentage of wetted surface downstream for both rivers and associated waterbodies (cumwettedsurfacebothkm2) divided by land surface for all segments within the basin located at a same or lesser distance to the sea.

downstreamwettedsurface

Percentage of wetted surface downstream (cumwettedsurfacekm2) divided by land surface for all segments within the basin located at a same or lesser distance to the sea.

drainage_density_perm.

River length / surface of basin in the basin downstream (m-1)  Numeric, multiplied by $10^4$, truncated to 20  

ef_fishingmethod

Fishing method. See details in text and Briand et al (2022)

ef_wetted_area

Surface of the electrofishing station

emu

Eel management unit. See https://github.com/ices-eg/wg_WGEEL/wiki

hydraulicdensityperm2.

  Number of riversegments per surface of basin (m-2). Numeric Multiplied by 10^6, truncated to 1.5

idsegment

Unique identifier of the segment TEXT

laltitudem.

Log transformed value of altitude (truncated)

lcs_height_10_n.

Log transformed value of cumulated height

lddws

Log transformed value of downstdrainagewettedsurfaceboth.

ldownstreamwettedsurface

Log of previous column

lriverwidthm.

Log transformed value of river width

month

Month

NCS

Number of eels estimated by Carle and Strub

ob_id

Operation (observation) id

op_id

Station (observation place) id

riverwidthm

Width of the river in m (comes from various sources see Atlas and Briand et al 2022).

seaidsegment

Identifier of the sea idsegment

temperature

Average temperature from 1960-2000 from the CCM (Vogt 2007)

temperature.1

duplicate of temperature

transport

code of transport operation

year

year of electrofishing

2.2. SIZE STRUCTURE OF EELS 

table_ind.Rdata A dataset of  494163 lines. In this dataset, one line correspond to one eel.

altitudem

Altitude in meter

altitudem.

Altitude in meter truncated to 800 m

area_sudo

Area for recruitment (Drouineau et al., 2021)

basin

Name (or code from bd_carthage France) of the basin

codesea

Code of the Sea, factor A = Atlantic, M = Mediterranean

country

A factor (FR, SP, PT) for France, Portugral and Spain

cs_height_08_n

Cumulated height from the sea,  dam height transformed with power 0.8, no prediction for missing values.

cs_height_08_n.

Same variable but truncated to 300

cs_height_08_p

Cumulated height from the sea,  dam height transformed with power 0.8, with prediction for missing values.

cs_height_08_p.

Same variable but truncated to 300

cs_height_08_pp

Cumulated height from the sea,  dam height transformed with power 0.8, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel

cs_height_08_pps

Cumulated height from the sea,  dam height transformed with power 0.8, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure

cs_height_10_FR

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from France are considered when building on a transnational water course.

cs_height_10_n

Cumulated height from the sea, no transformation, no prediction for missing values.

cs_height_10_n.

Same variable but truncated to 200

cs_height_10_p

Cumulated height from the sea, no transformation, missing height are extrapolated from two different models in France and the Iberian Peninsula

cs_height_10_p.

Same variable but truncated to 200

cs_height_10_pass0

Cumulated height from the sea, no transformation, including prediction for missing values, only the dams with pass are used to build the cumulated value.

cs_height_10_pass1

Cumulated height from the sea, no transformation, including prediction for missing values, only the dams without pass are used to build the cumulated value.

cs_height_10_pp

Cumulated height from the sea, no transformation,  with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel

cs_height_10_ppass0

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams with pass are used to build the cumulated value.

cs_height_10_ppass1

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams without pass are used to build the cumulated value.

cs_height_10_pps

Cumulated height from the sea, no transformation,  with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure

cs_height_10_pscore0

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams with score (that have been expertised as no or small barrier for eel)  are used to build the cumulated value.

cs_height_10_pscore1

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams without score are used to build the cumulated value.

cs_height_10_PT

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from Portugal are considered when building on a transnational water course.

cs_height_10_score0

Cumulated height from the sea, no transformation, including prediction for missing values, only the dams with score (that have been expertised as no or small barrier for eel)  are used to build the cumulated value.

cs_height_10_score1

Cumulated height from the sea, no transformation, including prediction for missing values, only the dams without score are used to build the cumulated value.

cs_height_10_SP

Cumulated height from the sea, no transformation, no prediction for missing values, only the dams from Spain are considered when building on a transnational water course.

cs_height_12_n

Cumulated height from the sea,  dam height transformed with power 1.2, no prediction for missing values.

cs_height_12_n.

Same variable but truncated to 500

cs_height_12_p

Cumulated height from the sea,  dam height transformed with power 1.2, with prediction for missing values.

cs_height_12_p.

Same variable but truncated to 500

cs_height_12_pp

Cumulated height from the sea,  dam height transformed with power 1.2, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel

cs_height_12_pps

Cumulated height from the sea,  dam height transformed with power 1.2, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure

cs_height_15_n

Cumulated height from the sea,  dam height transformed with power 1.5, no prediction for missing values.

cs_height_15_n.

Same variable but truncated to 800

cs_height_15_p

Cumulated height from the sea,  dam height transformed with power 1.5, with prediction for missing values.

cs_height_15_p.

Same variable but truncated to 800

cs_height_15_pp

Cumulated height from the sea,  dam height transformed with power 1.5, with prediction for missing values, the height of dam is set to zero if equiped with an efficient fishway for eel

cs_height_15_pps

Cumulated height from the sea,  dam height transformed with power 1.5, with prediction for missing values, the height of dam is set to zero if a score of efficient passage was attributed for eel on this structure

cumheightdam

Cumulated height of dam (ignore)

cumnbdamp

Cumulated number of dam from the sea

cumnbdamso

Cumulated number of dam from the sea only for dams whose height is larger than zero

densCS

Density from Carle and Strub, number in second pass extrapolated from efficiency if only one pass.

dist_from_gibraltar_km

Distance to Gibraltar calculated using an enveloppe along the coastline (e.g. the estuaries ingress inland are not counted for this distance).

distanceseakm

Distance to the sea in km

distanceseakm.

Distance to the sea, truncated at 500

distanceseam

Distance to the sea in m

distancesourcem

Distance to the source in m

ef_electrofishing_mean

Percentage of wetted surface downstream (cumwettedsurfacekm2) divided by land surface for all segments within the basin located at a same or lesser distance to the sea.

ef_fished_length

Length of the fishing operation

ef_fished_width

Width of the fishing operation

ef_fishingmethod

Method of electrofishing

ef_nbpas

Number of pass in the electrofishing operation

ef_wetted_area

Surface of the electrofishing station

emu

Eel management unit

id

Comes from uncout R function, which transforms counts into lines

idsegment

Unique identifier of the segment TEXT

isendoreic

Is the riversegment coming from an endoreic river ?

issea

Is the riversegment a sea outlet ?

laltitudem.

Log transformed value of altitude (truncated)

lcs_height_10_n.

Log transformed value of cumulated height

lengthm

Length of the electroshing station in m

lengthriverm

length of the riversegment in m

lriverwidthm.

Log transformed value of river width

medianflowm3ps

Median flow of the river in cubic meter per second

month

Month

name

Name of the river (Spain and Portugal)

nb_size_measured

Number of size measured in the electrofishing operation

nbp1

Number of eel collected in the first pass

nbp2

Number of eel collected in the second pass

nbp3

Number of eel collected in the third pass

NCS

Number estimated during the electrofishing operation by Carle and Strubb and interpolation of first pass efficiency if only one pass

nextdownidsegment

Code of the next downstream idsegment

Npred

Number of eel predicted on the riversegment pdeltagamma * watersurface

ob_dp_name

Data provider for the operation

ob_id

Operation (observation) id

ob_starting_date

Date of the operation

op_id

Station (observation place) id

pdelta

prediction of the delta (presence absence model)

pdeltagamma

pdelta*pgamma

pgamma

prediction of the gamma (positive densities model)

rdelta

residuals of the delta (presence absence model)

rdeltagamma

rdelta*rgamma

rgamma

residuals of the gamma (positive densities model)

riverwidthm

River width in m

riverwidthm.

same variable as riverwidthm (no truncation for riverwidth)

rN

residuals in number (difference in number of eels between observed and predicted there are some NA where we had to get the data from "density" as there was no water surface available....

seaidsegment

Identifier of the sea idsegment

sector

please ignore

shreeve

Shreve rank of the segment

size

Size class, 1 - <150      "2 - [150-300[" "3 - [300-450[" "4 - [450-600[" "5 - [600-750[" "6 - >=750" 

strahler

Strahler rank of the segment

surfacebvkm2

surface of the watershed in m2

surfacebvm2

surface of the watershed in km3

surfaceunitbvm2

surface of the unit basin surrounding the segment in m2

temperature

Average temperature from 1960-2000 from the CCM (Vogt 2007)

temperaturejan

January temperature (France)

temperaturejul

July temperature (France)

totalnumber

Total number of eel caught during the operation

transport

transport area

wettedsurfacem2

Surface of water downstream from the segment in the river. Corresponds only to rivers

wettedsurfaceotherm2

Surface of water downstream from the segment in the river. Corresponds only waterbodies (water surfaces, associated with the segment).

year

Year of electrofishing operation

2.3. Silver eel data

silver_eel_2020.Rdata

A dataset of  20101 lines corresponding to yellow and silver eel along with their measurements for silvering for eel > 150 mm.

This dataset has been built here, and validated here and here, For more information look at the report especially the annexes.

The columns are :

BL

Body length.

Dv

Vertical eye diameter.

FL

Pectoral fin length.

MD

Mean eye diameter.

W

Eel weight.

contrast

Body contrast for the eel.

Dh

Horizontal eye diameter.

diam_max

Max of horizontal and vertical eye  diameter.

diam_min

Min of horizontal and vertical eye  diameter.

distance_foyer_c

sqrt(diam_max^2 - diam_min^2).

excentricite

Eye excentricity = distance_foyer_c / diam_max.

IO

Occular index Pankhurst  = 100*((Dh+Dv/2)^2*pi/BL.

K_ful

Fulton coefficient= 100*W/(BL/10)^3.

maturite_durif

Durif 2009 maturity class.

oc_surface

Occular surface.

sexe_durif

Sex according to Durif 2009.

silver

Boolean, is it a silver eel, corresponds to one of "MII", "FIV", "FV" in Durif stage.

stade_pankhurst

Stage according to  Pankhurst.

stage_Durif

I,   MII, FII, FIII, FIV, FV see Durif 2009.

pdeltagamma

Density predicted from the delta gamma model in EDA (Briand et al, 2022).

dist_from_gibraltar_km

Distance from Gibraltar along the coastline, negative in the Mediterranean.

surfacebvm2

Surface of the watershed in m2.

altitudem.

Altitude in m truncated at 400.

temperature

Average temperature from 1960-2000 from the CCM (Vogt 2007).

distanceseakm.

Distance to the sea in km truncated at 500.

strahler

Strahler order of the stream.

month2

Month of electrofishing with values grouped for <=7 or >=10.

month

Month of electrofishing.

year

Year of electrofishing.

REFERENCES

Briand, C., Mateo, M., Drouineau, H., Maria, K., Diaz, E., and Beaulaton, L. (n.d.). Eel Density Analysis (EDA 2.3) Escapement of silver eels (Anguilla anguilla) from French, Spanish and Portuguese rivers. 

Drouineau, H., Marie, V., Diaz, E., Maria, M. S., Maria, K., Carlos, A., Fernández-Delgado, C., et al. 2021. Incorporating Stakeholder Knowledge Into a Complex Stock Assessment Model, the Case of Eel Recruitment. Preprints. https://www.preprints.org/manuscript/202104.0429/v1.

Durif, C. M., Guibert, A., and Elie, P. 2009. Morphological discrimination of the silvering stages of the European eel. In American Fisheries Society Symposium, pp. 103–111. http://fishlarvae.org/common/SiteMedia/durif%20et%20al%202009b.pdf.

Vogt, J., Soille, P., Jager, A. de, Rimaviciute, E., Mehl, W., Foisneau, S., Bodis, K., et al. 2007. A pan-European river and catchment database. Joint Research Centre-Institute for Environment and Sustainability, Luxembourg. http://www.envia.bl.uk/handle/123456789/4185.